User: Johannes Rainer

gravatar for Johannes Rainer
Johannes Rainer1.5k
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Italy
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@jotsetung
Last seen:
2 weeks, 3 days ago
Joined:
4 years, 9 months ago
Email:
j**************@eurac.edu

PhD, Bioinformatics Group, Institute for Biomedicine, Eurac Research, Bolzano, Italy

 

Posts by Johannes Rainer

<prev • 273 results • page 1 of 28 • next >
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Comment: C: xcms centwave roiList error
... Note that you can also provide a `matrix` with arguments `mz` and `rt` (two columns with lower and upper boundary, each row defining the region in wich you expect the data from one ion). With that you could extract multiple XIC at once and you could also run the `findChromPeaks` on all of them. That ...
written 17 days ago by Johannes Rainer1.5k
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Comment: C: xcms centwave roiList error
... The `findChromPeaks` function is really only intended to identify chromatographic peaks - not to extract ion chromatograms. To extract ion chromatograms you have to use the `chromatogram` function on the *on disk* data. It will extract the chromatogram for each file in your data. If you call `plot` ...
written 18 days ago by Johannes Rainer1.5k
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Answer: A: xcms centwave roiList error
... The `roiList` parameter should be a `list`. So what you should do is to provide the ROI as: ``` Trypto <- list(c(scmin = 51, scmax = 800, mzmin = 216.1321, mzmax = 216.1361, length = 20, intensity = 1000)) cwp <- CentWaveParam(roiList = Trypto) ``` Note however that it would be much easier t ...
written 19 days ago by Johannes Rainer1.5k
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Answer: A: Extracting Data from MSn experiment data ("OnDiskMSnExp")
... Hi James, the reason the `write.table` function takes so long is that in that call all processings are applied to the data. In the *on disk* mode all data manipulation operations are *cached* and only applied whenever you access the data (which in your case is when you call `write.table`, which in ...
written 19 days ago by Johannes Rainer1.5k
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Comment: C: XCMS - cannot allocate vector of size **Gb when global environment is empty
... Two things: 1) please change to the *new* functions/objects of `xcms` (see [xcms vignette](https://bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html)). 2) `profstep = 0.01` will create a huge matrix (which in your case will not fit into memory) - question is if you really nee ...
written 19 days ago by Johannes Rainer1.5k
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News: ensembldb EnsDb databases for Ensembl release 97 added to AnnotationHub
... Dear all, We've just added ensembldb `EnsDb` databases containing annotation from Ensembl for all 169 species in Ensembl release 97 to `AnnotationHub`: ``` > library(AnnotationHub) > ah <- AnnotationHub() snapshotDate(): 2019-05-02 > query(ah, c("EnsDb", "v97")) AnnotationHub with 169 ...
annotation news ensembl ensembldb written 5 weeks ago by Johannes Rainer1.5k
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Comment: C: Best alternative annotation package to BiomaRt
... You are right, the `EnsDb` databases that I provide as a *package* are outdated. But you can get `EnsDb` databases from `AnnotationHub` for all Ensembl releases from version 87 on: ``` > library(AnnotationHub) > library(ensembldb) > ah <- AnnotationHub() snapshotDate(): 2019-05-02 > ...
written 6 weeks ago by Johannes Rainer1.5k
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Answer: A: Gene biotype for a given symbol
... You can get that information using `ensembldb`: Assuming you're working with human annotations and want to use Ensembl release 86: ``` library(EnsDb.Hsapiens.v86) edb <- EnsDb.Hsapiens.v86 ## Get the transcript biotype for the gene SMC4 genes(edb, filter = ~ symbol == "SMC4", return.type = "Da ...
written 9 weeks ago by Johannes Rainer1.5k
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Comment: C: Getting CDSCHROM values from ENSEMBL/SYMBOL keys using mapIds from TxDb.Hsapiens
... Just a small comment to James' excellent answer: if your alignment/gene annotations were based on a specific Ensembl release, you should also ensure that you are loading/adding annotations from the same release. Example, your object is based on Ensembl release 91 data, then you would want to get the ...
written 4 months ago by Johannes Rainer1.5k
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Comment: C: mzR unable to open uncorrupted mzXML file
... Before digging into the error message I would make sure that you have all the most recent package versions and that all files are really there. So, please run `BiocManager::install()` to update potentially outdated packages and then `all(file.exists(files))`. You say you have ~ 1500 files, so mayb ...
written 4 months ago by Johannes Rainer1.5k

Latest awards to Johannes Rainer

Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Scholar 7 months ago, created an answer that has been accepted. For A: Ensembl plants at annotationHub?
Scholar 7 months ago, created an answer that has been accepted. For A: Retrieve canonical transcript for each gene via ensembldb R package
Popular Question 9 months ago, created a question with more than 1,000 views. For reactome.db: reactome IDs not mapped to pathway names
Popular Question 9 months ago, created a question with more than 1,000 views. For How to get from xcmsRaw to a xcmsSet
Popular Question 9 months ago, created a question with more than 1,000 views. For Reading alignments above a mapq threshold from BAM files
Scholar 9 months ago, created an answer that has been accepted. For A: biomaRt package problem
Popular Question 10 months ago, created a question with more than 1,000 views. For Plot data from VCF using Gviz?
Popular Question 11 months ago, created a question with more than 1,000 views. For Problem with biomart's listMarts function
Popular Question 14 months ago, created a question with more than 1,000 views. For Plot data from VCF using Gviz?
Popular Question 14 months ago, created a question with more than 1,000 views. For reactome.db: reactome IDs not mapped to pathway names
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Is it possible to annotated mitochondrial genes with ENSEMBL ids and Homo.sapien
Appreciated 2.1 years ago, created a post with more than 5 votes. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Appreciated 2.1 years ago, created a post with more than 5 votes. For A: makeTxDbFromBiomart Error: 1: Space required after the Public Identifier
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Plot data from VCF using Gviz?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For reactome.db: reactome IDs not mapped to pathway names
Guru 2.1 years ago, received more than 100 upvotes.
Voter 2.1 years ago, voted more than 100 times.
Scholar 2.1 years ago, created an answer that has been accepted. For A: Is it possible to annotated mitochondrial genes with ENSEMBL ids and Homo.sapien
Scholar 2.1 years ago, created an answer that has been accepted. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Scholar 2.1 years ago, created an answer that has been accepted. For A: Programatically download correct genome wide annotation package for given organi
Scholar 2.1 years ago, created an answer that has been accepted. For A: Is it possible to get Ensembl gene descriptions with ensembldb?
Scholar 2.2 years ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Great Question 2.2 years ago, created a question with more than 5,000 views. For Problem with biomart's listMarts function

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